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<td valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial">&nbsp;<br><big><big><strong><a href="src.html"><font color="#ffffff">src</font></a>.topology</strong></big></big> (12 November 2008)</font></td
><td align=right valign=bottom
><font color="#ffffff" face="helvetica, arial"><a href=".">index</a><br><a href="file:/Users/d3y382/workspaces/apbs/pdb2pqr/branches/pdb2pqr-1.7.1a/src/topology.py">/Users/d3y382/workspaces/apbs/pdb2pqr/branches/pdb2pqr-1.7.1a/src/topology.py</a></font></td></tr></table>
    <p><tt>Parser&nbsp;for&nbsp;TOPOLOGY.xml<br>
&nbsp;<br>
----------------------------<br>
&nbsp;<br>
PDB2PQR&nbsp;--&nbsp;An&nbsp;automated&nbsp;pipeline&nbsp;for&nbsp;the&nbsp;setup,&nbsp;execution,&nbsp;and&nbsp;analysis&nbsp;of<br>
Poisson-Boltzmann&nbsp;electrostatics&nbsp;calculations<br>
&nbsp;<br>
Copyright&nbsp;(c)&nbsp;2002-2011,&nbsp;Jens&nbsp;Erik&nbsp;Nielsen,&nbsp;University&nbsp;College&nbsp;Dublin;&nbsp;<br>
Nathan&nbsp;A.&nbsp;Baker,&nbsp;Battelle&nbsp;Memorial&nbsp;Institute,&nbsp;Developed&nbsp;at&nbsp;the&nbsp;Pacific&nbsp;<br>
Northwest&nbsp;National&nbsp;Laboratory,&nbsp;operated&nbsp;by&nbsp;Battelle&nbsp;Memorial&nbsp;Institute,&nbsp;<br>
Pacific&nbsp;Northwest&nbsp;Division&nbsp;for&nbsp;the&nbsp;U.S.&nbsp;Department&nbsp;Energy.;&nbsp;<br>
Paul&nbsp;Czodrowski&nbsp;&amp;&nbsp;Gerhard&nbsp;Klebe,&nbsp;University&nbsp;of&nbsp;Marburg.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;All&nbsp;rights&nbsp;reserved.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;Redistribution&nbsp;and&nbsp;use&nbsp;in&nbsp;source&nbsp;and&nbsp;binary&nbsp;forms,&nbsp;with&nbsp;or&nbsp;without&nbsp;modification,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;are&nbsp;permitted&nbsp;provided&nbsp;that&nbsp;the&nbsp;following&nbsp;conditions&nbsp;are&nbsp;met:<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Redistributions&nbsp;of&nbsp;source&nbsp;code&nbsp;must&nbsp;retain&nbsp;the&nbsp;above&nbsp;copyright&nbsp;notice,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;this&nbsp;list&nbsp;of&nbsp;conditions&nbsp;and&nbsp;the&nbsp;following&nbsp;disclaimer.<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Redistributions&nbsp;in&nbsp;binary&nbsp;form&nbsp;must&nbsp;reproduce&nbsp;the&nbsp;above&nbsp;copyright&nbsp;notice,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;this&nbsp;list&nbsp;of&nbsp;conditions&nbsp;and&nbsp;the&nbsp;following&nbsp;disclaimer&nbsp;in&nbsp;the&nbsp;documentation&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;and/or&nbsp;other&nbsp;materials&nbsp;provided&nbsp;with&nbsp;the&nbsp;distribution.<br>
&nbsp;&nbsp;&nbsp;&nbsp;*&nbsp;Neither&nbsp;the&nbsp;names&nbsp;of&nbsp;University&nbsp;College&nbsp;Dublin,&nbsp;Battelle&nbsp;Memorial&nbsp;Institute,<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;Pacific&nbsp;Northwest&nbsp;National&nbsp;Laboratory,&nbsp;US&nbsp;Department&nbsp;of&nbsp;Energy,&nbsp;or&nbsp;University<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;of&nbsp;Marburg&nbsp;nor&nbsp;the&nbsp;names&nbsp;of&nbsp;its&nbsp;contributors&nbsp;may&nbsp;be&nbsp;used&nbsp;to&nbsp;endorse&nbsp;or&nbsp;promote<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;products&nbsp;derived&nbsp;from&nbsp;this&nbsp;software&nbsp;without&nbsp;specific&nbsp;prior&nbsp;written&nbsp;permission.<br>
&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;THIS&nbsp;SOFTWARE&nbsp;IS&nbsp;PROVIDED&nbsp;BY&nbsp;THE&nbsp;COPYRIGHT&nbsp;HOLDERS&nbsp;AND&nbsp;CONTRIBUTORS&nbsp;"AS&nbsp;IS"&nbsp;AND&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;ANY&nbsp;EXPRESS&nbsp;OR&nbsp;IMPLIED&nbsp;WARRANTIES,&nbsp;INCLUDING,&nbsp;BUT&nbsp;NOT&nbsp;LIMITED&nbsp;TO,&nbsp;THE&nbsp;IMPLIED&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;WARRANTIES&nbsp;OF&nbsp;MERCHANTABILITY&nbsp;AND&nbsp;FITNESS&nbsp;FOR&nbsp;A&nbsp;PARTICULAR&nbsp;PURPOSE&nbsp;ARE&nbsp;DISCLAIMED.&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;IN&nbsp;NO&nbsp;EVENT&nbsp;SHALL&nbsp;THE&nbsp;COPYRIGHT&nbsp;OWNER&nbsp;OR&nbsp;CONTRIBUTORS&nbsp;BE&nbsp;LIABLE&nbsp;FOR&nbsp;ANY&nbsp;DIRECT,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;INDIRECT,&nbsp;INCIDENTAL,&nbsp;SPECIAL,&nbsp;EXEMPLARY,&nbsp;OR&nbsp;CONSEQUENTIAL&nbsp;DAMAGES&nbsp;(INCLUDING,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;BUT&nbsp;NOT&nbsp;LIMITED&nbsp;TO,&nbsp;PROCUREMENT&nbsp;OF&nbsp;SUBSTITUTE&nbsp;GOODS&nbsp;OR&nbsp;SERVICES;&nbsp;LOSS&nbsp;OF&nbsp;USE,&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;DATA,&nbsp;OR&nbsp;PROFITS;&nbsp;OR&nbsp;BUSINESS&nbsp;INTERRUPTION)&nbsp;HOWEVER&nbsp;CAUSED&nbsp;AND&nbsp;ON&nbsp;ANY&nbsp;THEORY&nbsp;OF&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;LIABILITY,&nbsp;WHETHER&nbsp;IN&nbsp;CONTRACT,&nbsp;STRICT&nbsp;LIABILITY,&nbsp;OR&nbsp;TORT&nbsp;(INCLUDING&nbsp;NEGLIGENCE&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;OR&nbsp;OTHERWISE)&nbsp;ARISING&nbsp;IN&nbsp;ANY&nbsp;WAY&nbsp;OUT&nbsp;OF&nbsp;THE&nbsp;USE&nbsp;OF&nbsp;THIS&nbsp;SOFTWARE,&nbsp;EVEN&nbsp;IF&nbsp;ADVISED&nbsp;<br>
&nbsp;&nbsp;&nbsp;&nbsp;OF&nbsp;THE&nbsp;POSSIBILITY&nbsp;OF&nbsp;SUCH&nbsp;DAMAGE.<br>
&nbsp;<br>
----------------------------</tt></p>
<p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#aa55cc">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Modules</strong></big></font></td></tr>
    
<tr><td bgcolor="#aa55cc"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><table width="100%" summary="list"><tr><td width="25%" valign=top><a href="xml.sax.html">xml.sax</a><br>
</td><td width="25%" valign=top></td><td width="25%" valign=top></td><td width="25%" valign=top></td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ee77aa">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Classes</strong></big></font></td></tr>
    
<tr><td bgcolor="#ee77aa"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><dl>
<dt><font face="helvetica, arial"><a href="src.topology.html#Topology">Topology</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyAtom">TopologyAtom</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyConformer">TopologyConformer</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyConformerAdd">TopologyConformerAdd</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyConformerRemove">TopologyConformerRemove</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyDihedral">TopologyDihedral</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyReference">TopologyReference</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyResidue">TopologyResidue</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyTautomer">TopologyTautomer</a>
</font></dt><dt><font face="helvetica, arial"><a href="src.topology.html#TopologyTitrationState">TopologyTitrationState</a>
</font></dt><dt><font face="helvetica, arial"><a href="xml.sax.handler.html#ContentHandler">xml.sax.handler.ContentHandler</a>
</font></dt><dd>
<dl>
<dt><font face="helvetica, arial"><a href="src.topology.html#TopologyHandler">TopologyHandler</a>
</font></dt></dl>
</dd>
</dl>
 <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="Topology">class <strong>Topology</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Contains&nbsp;the&nbsp;structured&nbsp;definitions&nbsp;of&nbsp;residue&nbsp;reference&nbsp;coordinates&nbsp;as&nbsp;well&nbsp;as&nbsp;alternate&nbsp;titration,&nbsp;<br>
conformer,&nbsp;and&nbsp;tautomer&nbsp;states.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="Topology-__init__"><strong>__init__</strong></a>(self, topologyFile)</dt><dd><tt>Initialize&nbsp;with&nbsp;the&nbsp;topology&nbsp;file&nbsp;reference&nbsp;ready&nbsp;for&nbsp;reading</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TopologyAtom">class <strong>TopologyAtom</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>A&nbsp;class&nbsp;for&nbsp;atom&nbsp;topology&nbsp;information<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyAtom-__init__"><strong>__init__</strong></a>(self, parent)</dt><dd><tt>Needs&nbsp;to&nbsp;be&nbsp;intialized&nbsp;with&nbsp;an&nbsp;upper-level&nbsp;class&nbsp;that&nbsp;contains&nbsp;an&nbsp;atoms&nbsp;array&nbsp;(e.g.,&nbsp;<a href="#TopologyReference">TopologyReference</a><br>
or&nbsp;TopologyConformerAddition)</tt></dd></dl>

<dl><dt><a name="TopologyAtom-__str__"><strong>__str__</strong></a>(self)</dt></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TopologyConformer">class <strong>TopologyConformer</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>A&nbsp;class&nbsp;for&nbsp;topology&nbsp;conformer&nbsp;information<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyConformer-__init__"><strong>__init__</strong></a>(self, topologyTautomer)</dt><dd><tt>Initialize&nbsp;with&nbsp;a&nbsp;<a href="#TopologyTautomer">TopologyTautomer</a>&nbsp;object</tt></dd></dl>

<dl><dt><a name="TopologyConformer-__str__"><strong>__str__</strong></a>(self)</dt></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TopologyConformerAdd">class <strong>TopologyConformerAdd</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>A&nbsp;class&nbsp;for&nbsp;adding&nbsp;atoms&nbsp;to&nbsp;a&nbsp;conformer<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyConformerAdd-__init__"><strong>__init__</strong></a>(self, topologyConformer)</dt><dd><tt>Initialize&nbsp;with&nbsp;a&nbsp;<a href="#TopologyConformer">TopologyConformer</a>&nbsp;object</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TopologyConformerRemove">class <strong>TopologyConformerRemove</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>A&nbsp;class&nbsp;for&nbsp;removing&nbsp;atoms&nbsp;to&nbsp;a&nbsp;conformer<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyConformerRemove-__init__"><strong>__init__</strong></a>(self, topologyConformer)</dt><dd><tt>Initialize&nbsp;with&nbsp;a&nbsp;<a href="#TopologyConformer">TopologyConformer</a>&nbsp;object</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TopologyDihedral">class <strong>TopologyDihedral</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>A&nbsp;class&nbsp;for&nbsp;dihedral&nbsp;topology&nbsp;information.<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyDihedral-__init__"><strong>__init__</strong></a>(self, parent)</dt><dd><tt>Needs&nbsp;a&nbsp;parent&nbsp;that&nbsp;has&nbsp;a&nbsp;dihedral&nbsp;list.</tt></dd></dl>

<dl><dt><a name="TopologyDihedral-__str__"><strong>__str__</strong></a>(self)</dt></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TopologyHandler">class <strong>TopologyHandler</strong></a>(<a href="xml.sax.handler.html#ContentHandler">xml.sax.handler.ContentHandler</a>)</font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>Handler&nbsp;for&nbsp;XML-based&nbsp;topology&nbsp;files.&nbsp;&nbsp;Assumes&nbsp;the&nbsp;following&nbsp;hierarchy&nbsp;of&nbsp;tags:<br>
topology<br>
--&gt;residue<br>
&nbsp;&nbsp;&nbsp;|--&gt;reference<br>
&nbsp;&nbsp;&nbsp;|--&gt;titrationstate<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;|--&gt;tautomer<br>
&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;|--&gt;conformer<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyHandler-__init__"><strong>__init__</strong></a>(self)</dt></dl>

<dl><dt><a name="TopologyHandler-characters"><strong>characters</strong></a>(self, text)</dt></dl>

<dl><dt><a name="TopologyHandler-endElement"><strong>endElement</strong></a>(self, tagName)</dt></dl>

<dl><dt><a name="TopologyHandler-startElement"><strong>startElement</strong></a>(self, tagName, attributes)</dt></dl>

<hr>
Methods inherited from <a href="xml.sax.handler.html#ContentHandler">xml.sax.handler.ContentHandler</a>:<br>
<dl><dt><a name="TopologyHandler-endDocument"><strong>endDocument</strong></a>(self)</dt><dd><tt>Receive&nbsp;notification&nbsp;of&nbsp;the&nbsp;end&nbsp;of&nbsp;a&nbsp;document.<br>
&nbsp;<br>
The&nbsp;SAX&nbsp;parser&nbsp;will&nbsp;invoke&nbsp;this&nbsp;method&nbsp;only&nbsp;once,&nbsp;and&nbsp;it&nbsp;will<br>
be&nbsp;the&nbsp;last&nbsp;method&nbsp;invoked&nbsp;during&nbsp;the&nbsp;parse.&nbsp;The&nbsp;parser&nbsp;shall<br>
not&nbsp;invoke&nbsp;this&nbsp;method&nbsp;until&nbsp;it&nbsp;has&nbsp;either&nbsp;abandoned&nbsp;parsing<br>
(because&nbsp;of&nbsp;an&nbsp;unrecoverable&nbsp;error)&nbsp;or&nbsp;reached&nbsp;the&nbsp;end&nbsp;of<br>
input.</tt></dd></dl>

<dl><dt><a name="TopologyHandler-endElementNS"><strong>endElementNS</strong></a>(self, name, qname)</dt><dd><tt>Signals&nbsp;the&nbsp;end&nbsp;of&nbsp;an&nbsp;element&nbsp;in&nbsp;namespace&nbsp;mode.<br>
&nbsp;<br>
The&nbsp;name&nbsp;parameter&nbsp;contains&nbsp;the&nbsp;name&nbsp;of&nbsp;the&nbsp;element&nbsp;type,&nbsp;just<br>
as&nbsp;with&nbsp;the&nbsp;startElementNS&nbsp;event.</tt></dd></dl>

<dl><dt><a name="TopologyHandler-endPrefixMapping"><strong>endPrefixMapping</strong></a>(self, prefix)</dt><dd><tt>End&nbsp;the&nbsp;scope&nbsp;of&nbsp;a&nbsp;prefix-URI&nbsp;mapping.<br>
&nbsp;<br>
See&nbsp;startPrefixMapping&nbsp;for&nbsp;details.&nbsp;This&nbsp;event&nbsp;will&nbsp;always<br>
occur&nbsp;after&nbsp;the&nbsp;corresponding&nbsp;endElement&nbsp;event,&nbsp;but&nbsp;the&nbsp;order<br>
of&nbsp;endPrefixMapping&nbsp;events&nbsp;is&nbsp;not&nbsp;otherwise&nbsp;guaranteed.</tt></dd></dl>

<dl><dt><a name="TopologyHandler-ignorableWhitespace"><strong>ignorableWhitespace</strong></a>(self, whitespace)</dt><dd><tt>Receive&nbsp;notification&nbsp;of&nbsp;ignorable&nbsp;whitespace&nbsp;in&nbsp;element&nbsp;content.<br>
&nbsp;<br>
Validating&nbsp;Parsers&nbsp;must&nbsp;use&nbsp;this&nbsp;method&nbsp;to&nbsp;report&nbsp;each&nbsp;chunk<br>
of&nbsp;ignorable&nbsp;whitespace&nbsp;(see&nbsp;the&nbsp;W3C&nbsp;XML&nbsp;1.0&nbsp;recommendation,<br>
section&nbsp;2.10):&nbsp;non-validating&nbsp;parsers&nbsp;may&nbsp;also&nbsp;use&nbsp;this&nbsp;method<br>
if&nbsp;they&nbsp;are&nbsp;capable&nbsp;of&nbsp;parsing&nbsp;and&nbsp;using&nbsp;content&nbsp;models.<br>
&nbsp;<br>
SAX&nbsp;parsers&nbsp;may&nbsp;return&nbsp;all&nbsp;contiguous&nbsp;whitespace&nbsp;in&nbsp;a&nbsp;single<br>
chunk,&nbsp;or&nbsp;they&nbsp;may&nbsp;split&nbsp;it&nbsp;into&nbsp;several&nbsp;chunks;&nbsp;however,&nbsp;all<br>
of&nbsp;the&nbsp;characters&nbsp;in&nbsp;any&nbsp;single&nbsp;event&nbsp;must&nbsp;come&nbsp;from&nbsp;the&nbsp;same<br>
external&nbsp;entity,&nbsp;so&nbsp;that&nbsp;the&nbsp;Locator&nbsp;provides&nbsp;useful<br>
information.</tt></dd></dl>

<dl><dt><a name="TopologyHandler-processingInstruction"><strong>processingInstruction</strong></a>(self, target, data)</dt><dd><tt>Receive&nbsp;notification&nbsp;of&nbsp;a&nbsp;processing&nbsp;instruction.<br>
&nbsp;<br>
The&nbsp;Parser&nbsp;will&nbsp;invoke&nbsp;this&nbsp;method&nbsp;once&nbsp;for&nbsp;each&nbsp;processing<br>
instruction&nbsp;found:&nbsp;note&nbsp;that&nbsp;processing&nbsp;instructions&nbsp;may&nbsp;occur<br>
before&nbsp;or&nbsp;after&nbsp;the&nbsp;main&nbsp;document&nbsp;element.<br>
&nbsp;<br>
A&nbsp;SAX&nbsp;parser&nbsp;should&nbsp;never&nbsp;report&nbsp;an&nbsp;XML&nbsp;declaration&nbsp;(XML&nbsp;1.0,<br>
section&nbsp;2.8)&nbsp;or&nbsp;a&nbsp;text&nbsp;declaration&nbsp;(XML&nbsp;1.0,&nbsp;section&nbsp;4.3.1)<br>
using&nbsp;this&nbsp;method.</tt></dd></dl>

<dl><dt><a name="TopologyHandler-setDocumentLocator"><strong>setDocumentLocator</strong></a>(self, locator)</dt><dd><tt>Called&nbsp;by&nbsp;the&nbsp;parser&nbsp;to&nbsp;give&nbsp;the&nbsp;application&nbsp;a&nbsp;locator&nbsp;for<br>
locating&nbsp;the&nbsp;origin&nbsp;of&nbsp;document&nbsp;events.<br>
&nbsp;<br>
SAX&nbsp;parsers&nbsp;are&nbsp;strongly&nbsp;encouraged&nbsp;(though&nbsp;not&nbsp;absolutely<br>
required)&nbsp;to&nbsp;supply&nbsp;a&nbsp;locator:&nbsp;if&nbsp;it&nbsp;does&nbsp;so,&nbsp;it&nbsp;must&nbsp;supply<br>
the&nbsp;locator&nbsp;to&nbsp;the&nbsp;application&nbsp;by&nbsp;invoking&nbsp;this&nbsp;method&nbsp;before<br>
invoking&nbsp;any&nbsp;of&nbsp;the&nbsp;other&nbsp;methods&nbsp;in&nbsp;the&nbsp;DocumentHandler<br>
interface.<br>
&nbsp;<br>
The&nbsp;locator&nbsp;allows&nbsp;the&nbsp;application&nbsp;to&nbsp;determine&nbsp;the&nbsp;end<br>
position&nbsp;of&nbsp;any&nbsp;document-related&nbsp;event,&nbsp;even&nbsp;if&nbsp;the&nbsp;parser&nbsp;is<br>
not&nbsp;reporting&nbsp;an&nbsp;error.&nbsp;Typically,&nbsp;the&nbsp;application&nbsp;will&nbsp;use<br>
this&nbsp;information&nbsp;for&nbsp;reporting&nbsp;its&nbsp;own&nbsp;errors&nbsp;(such&nbsp;as<br>
character&nbsp;content&nbsp;that&nbsp;does&nbsp;not&nbsp;match&nbsp;an&nbsp;application's<br>
business&nbsp;rules).&nbsp;The&nbsp;information&nbsp;returned&nbsp;by&nbsp;the&nbsp;locator&nbsp;is<br>
probably&nbsp;not&nbsp;sufficient&nbsp;for&nbsp;use&nbsp;with&nbsp;a&nbsp;search&nbsp;engine.<br>
&nbsp;<br>
Note&nbsp;that&nbsp;the&nbsp;locator&nbsp;will&nbsp;return&nbsp;correct&nbsp;information&nbsp;only<br>
during&nbsp;the&nbsp;invocation&nbsp;of&nbsp;the&nbsp;events&nbsp;in&nbsp;this&nbsp;interface.&nbsp;The<br>
application&nbsp;should&nbsp;not&nbsp;attempt&nbsp;to&nbsp;use&nbsp;it&nbsp;at&nbsp;any&nbsp;other&nbsp;time.</tt></dd></dl>

<dl><dt><a name="TopologyHandler-skippedEntity"><strong>skippedEntity</strong></a>(self, name)</dt><dd><tt>Receive&nbsp;notification&nbsp;of&nbsp;a&nbsp;skipped&nbsp;entity.<br>
&nbsp;<br>
The&nbsp;Parser&nbsp;will&nbsp;invoke&nbsp;this&nbsp;method&nbsp;once&nbsp;for&nbsp;each&nbsp;entity<br>
skipped.&nbsp;Non-validating&nbsp;processors&nbsp;may&nbsp;skip&nbsp;entities&nbsp;if&nbsp;they<br>
have&nbsp;not&nbsp;seen&nbsp;the&nbsp;declarations&nbsp;(because,&nbsp;for&nbsp;example,&nbsp;the<br>
entity&nbsp;was&nbsp;declared&nbsp;in&nbsp;an&nbsp;external&nbsp;DTD&nbsp;subset).&nbsp;All&nbsp;processors<br>
may&nbsp;skip&nbsp;external&nbsp;entities,&nbsp;depending&nbsp;on&nbsp;the&nbsp;values&nbsp;of&nbsp;the<br>
<a href="http://xml.org/sax/features/external-general-entities">http://xml.org/sax/features/external-general-entities</a>&nbsp;and&nbsp;the<br>
<a href="http://xml.org/sax/features/external-parameter-entities">http://xml.org/sax/features/external-parameter-entities</a><br>
properties.</tt></dd></dl>

<dl><dt><a name="TopologyHandler-startDocument"><strong>startDocument</strong></a>(self)</dt><dd><tt>Receive&nbsp;notification&nbsp;of&nbsp;the&nbsp;beginning&nbsp;of&nbsp;a&nbsp;document.<br>
&nbsp;<br>
The&nbsp;SAX&nbsp;parser&nbsp;will&nbsp;invoke&nbsp;this&nbsp;method&nbsp;only&nbsp;once,&nbsp;before&nbsp;any<br>
other&nbsp;methods&nbsp;in&nbsp;this&nbsp;interface&nbsp;or&nbsp;in&nbsp;DTDHandler&nbsp;(except&nbsp;for<br>
setDocumentLocator).</tt></dd></dl>

<dl><dt><a name="TopologyHandler-startElementNS"><strong>startElementNS</strong></a>(self, name, qname, attrs)</dt><dd><tt>Signals&nbsp;the&nbsp;start&nbsp;of&nbsp;an&nbsp;element&nbsp;in&nbsp;namespace&nbsp;mode.<br>
&nbsp;<br>
The&nbsp;name&nbsp;parameter&nbsp;contains&nbsp;the&nbsp;name&nbsp;of&nbsp;the&nbsp;element&nbsp;type&nbsp;as&nbsp;a<br>
(uri,&nbsp;localname)&nbsp;tuple,&nbsp;the&nbsp;qname&nbsp;parameter&nbsp;the&nbsp;raw&nbsp;XML&nbsp;1.0<br>
name&nbsp;used&nbsp;in&nbsp;the&nbsp;source&nbsp;document,&nbsp;and&nbsp;the&nbsp;attrs&nbsp;parameter<br>
holds&nbsp;an&nbsp;instance&nbsp;of&nbsp;the&nbsp;Attributes&nbsp;class&nbsp;containing&nbsp;the<br>
attributes&nbsp;of&nbsp;the&nbsp;element.<br>
&nbsp;<br>
The&nbsp;uri&nbsp;part&nbsp;of&nbsp;the&nbsp;name&nbsp;tuple&nbsp;is&nbsp;None&nbsp;for&nbsp;elements&nbsp;which&nbsp;have<br>
no&nbsp;namespace.</tt></dd></dl>

<dl><dt><a name="TopologyHandler-startPrefixMapping"><strong>startPrefixMapping</strong></a>(self, prefix, uri)</dt><dd><tt>Begin&nbsp;the&nbsp;scope&nbsp;of&nbsp;a&nbsp;prefix-URI&nbsp;Namespace&nbsp;mapping.<br>
&nbsp;<br>
The&nbsp;information&nbsp;from&nbsp;this&nbsp;event&nbsp;is&nbsp;not&nbsp;necessary&nbsp;for&nbsp;normal<br>
Namespace&nbsp;processing:&nbsp;the&nbsp;SAX&nbsp;XML&nbsp;reader&nbsp;will&nbsp;automatically<br>
replace&nbsp;prefixes&nbsp;for&nbsp;element&nbsp;and&nbsp;attribute&nbsp;names&nbsp;when&nbsp;the<br>
<a href="http://xml.org/sax/features/namespaces">http://xml.org/sax/features/namespaces</a>&nbsp;feature&nbsp;is&nbsp;true&nbsp;(the<br>
default).<br>
&nbsp;<br>
There&nbsp;are&nbsp;cases,&nbsp;however,&nbsp;when&nbsp;applications&nbsp;need&nbsp;to&nbsp;use<br>
prefixes&nbsp;in&nbsp;character&nbsp;data&nbsp;or&nbsp;in&nbsp;attribute&nbsp;values,&nbsp;where&nbsp;they<br>
cannot&nbsp;safely&nbsp;be&nbsp;expanded&nbsp;automatically;&nbsp;the<br>
start/endPrefixMapping&nbsp;event&nbsp;supplies&nbsp;the&nbsp;information&nbsp;to&nbsp;the<br>
application&nbsp;to&nbsp;expand&nbsp;prefixes&nbsp;in&nbsp;those&nbsp;contexts&nbsp;itself,&nbsp;if<br>
necessary.<br>
&nbsp;<br>
Note&nbsp;that&nbsp;start/endPrefixMapping&nbsp;events&nbsp;are&nbsp;not&nbsp;guaranteed&nbsp;to<br>
be&nbsp;properly&nbsp;nested&nbsp;relative&nbsp;to&nbsp;each-other:&nbsp;all<br>
startPrefixMapping&nbsp;events&nbsp;will&nbsp;occur&nbsp;before&nbsp;the&nbsp;corresponding<br>
startElement&nbsp;event,&nbsp;and&nbsp;all&nbsp;endPrefixMapping&nbsp;events&nbsp;will&nbsp;occur<br>
after&nbsp;the&nbsp;corresponding&nbsp;endElement&nbsp;event,&nbsp;but&nbsp;their&nbsp;order&nbsp;is<br>
not&nbsp;guaranteed.</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TopologyReference">class <strong>TopologyReference</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>A&nbsp;class&nbsp;for&nbsp;the&nbsp;reference&nbsp;structure&nbsp;of&nbsp;a&nbsp;residue<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyReference-__init__"><strong>__init__</strong></a>(self, topologyResidue)</dt><dd><tt>Initialize&nbsp;with&nbsp;a&nbsp;<a href="#TopologyResidue">TopologyResidue</a>&nbsp;object</tt></dd></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TopologyResidue">class <strong>TopologyResidue</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>A&nbsp;class&nbsp;for&nbsp;residue&nbsp;topology&nbsp;information<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyResidue-__init__"><strong>__init__</strong></a>(self, topology)</dt><dd><tt>Initialize&nbsp;with&nbsp;a&nbsp;<a href="#Topology">Topology</a>&nbsp;object</tt></dd></dl>

<dl><dt><a name="TopologyResidue-__str__"><strong>__str__</strong></a>(self)</dt></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TopologyTautomer">class <strong>TopologyTautomer</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>A&nbsp;class&nbsp;for&nbsp;topology&nbsp;tautomer&nbsp;information<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyTautomer-__init__"><strong>__init__</strong></a>(self, topologyTitrationState)</dt><dd><tt>Initialize&nbsp;with&nbsp;a&nbsp;<a href="#TopologyTitrationState">TopologyTitrationState</a>&nbsp;object</tt></dd></dl>

<dl><dt><a name="TopologyTautomer-__str__"><strong>__str__</strong></a>(self)</dt></dl>

</td></tr></table> <p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#ffc8d8">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#000000" face="helvetica, arial"><a name="TopologyTitrationState">class <strong>TopologyTitrationState</strong></a></font></td></tr>
    
<tr bgcolor="#ffc8d8"><td rowspan=2><tt>&nbsp;&nbsp;&nbsp;</tt></td>
<td colspan=2><tt>A&nbsp;class&nbsp;for&nbsp;the&nbsp;titration&nbsp;state&nbsp;of&nbsp;a&nbsp;residue<br>&nbsp;</tt></td></tr>
<tr><td>&nbsp;</td>
<td width="100%">Methods defined here:<br>
<dl><dt><a name="TopologyTitrationState-__init__"><strong>__init__</strong></a>(self, topologyResidue)</dt><dd><tt>Initialize&nbsp;with&nbsp;a&nbsp;<a href="#TopologyResidue">TopologyResidue</a>&nbsp;object</tt></dd></dl>

<dl><dt><a name="TopologyTitrationState-__str__"><strong>__str__</strong></a>(self)</dt></dl>

</td></tr></table></td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#55aa55">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Data</strong></big></font></td></tr>
    
<tr><td bgcolor="#55aa55"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%"><strong>TOPOLOGYPATH</strong> = 'TOPOLOGY.xml'<br>
<strong>__author__</strong> = 'Nathan Baker, Yong Huang'<br>
<strong>__date__</strong> = '12 November 2008'<br>
<strong>stderr</strong> = &lt;open file '&lt;stderr&gt;', mode 'w' at 0x100416140&gt;</td></tr></table><p>
<table width="100%" cellspacing=0 cellpadding=2 border=0 summary="section">
<tr bgcolor="#7799ee">
<td colspan=3 valign=bottom>&nbsp;<br>
<font color="#ffffff" face="helvetica, arial"><big><strong>Author</strong></big></font></td></tr>
    
<tr><td bgcolor="#7799ee"><tt>&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;&nbsp;</tt></td><td>&nbsp;</td>
<td width="100%">Nathan&nbsp;Baker,&nbsp;Yong&nbsp;Huang</td></tr></table>
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